Researchers Created a 3-D Map of 100 Million Cells in the Mouse Brain

Neuroscientists have been using the tool since 2017 to pinpoint where exactly their data are coming from

mouse brain
Researchers at the Allen Institute for Brain Science averaged the structures of 1,625 mouse brains to create a standard model. Courtesy of the Allen Institute for Brain Science

Researchers at the Allen Institute for Brain Science have accomplished a feat of cartography, creating a map of a standard mouse brain with details down to the cellular level.

The results, published on May 7 in the journal Cell, provide a 3-D atlas of an average mouse’s brain structure as a reference for neuroscientists everywhere. The new map is the third iteration of the project, and shows details with a new level of granularity, including over 800 brain structures and 100 million individual cells.

“We hope the wider neuroscience community will use it as a new standard reference atlas,” Allen Institute neuroscientist and co-author Lydia Ng tells James Lloyd at the BBC’s Science Focus.

Researchers can reference the 3-D map of the mouse brain to better understand which brain regions are activated during an experiment. Different structures in the brain have certain tasks. In humans, the fusiform area can spot a face, the amygdala is the fear center, and longtime players of the Pokémon franchise may even have a region committed to recognizing the game’s characters. The mouse brain atlas is the based on over 1,600 mouse brains, creating a standard template that clearly delineates hundreds of structures.

“We’ve created this really beautiful average mouse brain,” co-author David Feng told Spectrum’s Hannah Furfaro when the map was first presented at the Society for Neuroscience annual meeting in 2017. “What you see remaining after all the averaging we do is very sharp definitions of structures that are stereotypical, which means there’s not a lot of wiggle room anymore.”

Neuroscientists can then use the atlas to understand where exactly they’re seeing activity in their own experiments in mice. Scientists used to eyeball the region that a blip on a measurement tool was coming from, but as modern experiments collect an increasing amount of data, a digital tool for pinpointing a signal’s source became vital, Ng says in a statement. Researchers can also use the average brain model to compare the shape of the brain with mice that are bred to have conditions that affect the brain.

As Ryan Blethen reported for the Seattle Times last August, researchers at the Allen Institute are also working on projects clarifying the things that our brains have in common with mouse brains, and highlighting the differences. And in October, the institute announced the completion of a map of how the mouse brain is wired. The tools are all available online for ease of access in the neuroscience field.

“By making our atlas and related tools open access, new data and data types generated across our community can be more easily integrated and compared in the same spatial context,” Ng tells Science Focus, “and the atlas in turn can be modified as our knowledge about brain structure evolves.”

Because the tool was first released online in 2017, it’s already been used to complete some research. University of Washington neuroscientist Nick Steinmetz used the mouse brain atlas to analyze data from a project aimed at understanding how mice choose between images. The study, published in Nature in November, used the tool to understand where exactly the brain was active.

“The atlas was a really necessary resource that enabled the very idea of doing studies at the brain-wide level,” Steinmetz, who wasn’t involved with the new study but is associated with the Allen Institute, said in a statement. “When you’re recording from hundreds of sites across the brain, that introduces a new scale of investigation. You have to have a bigger view of where all the recording sites are, and the CCF [mouse brain map] is what made that possible.”

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